Method and system for detecting a target within a population of molecules

ABSTRACT

A method of detecting a target within a population of molecules comprising: contacting a plurality of labeled probe molecules with the population of molecules potentially containing a target of the probe molecules; acquiring a probe specific signal emitted by said labeled probe molecules that bound to said target together with a background signal; preferentially modulating said probe specific signal by at least one of modulating said acquisition and modulating an emission of said probe specific signal; and detecting said probe specific signal over said background signal using said preferential modulation.

RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.15/420,159 filed on Jan. 31, 2017, which is a continuation of U.S.patent application Ser. No. 13/909,109 filed on Jun. 4, 2013, now U.S.Pat. No. 9,575,068, which is a continuation of U.S. patent applicationSer. No. 12/312,071 filed on Apr. 24, 2009, now U.S. Pat. No. 8,465,989,which is a National Phase of PCT Patent Application No.PCT/IL2007/001287 having International Filing Date of Oct. 25, 2007,which claims the benefit of priority of U.S. Provisional PatentApplication No. 60/854,722 filed on Oct. 27, 2006. The contents of theabove applications are all incorporated by reference as if fully setforth herein in their entirety.

FIELD AND BACKGROUND OF THE INVENTION

The present invention relates to detecting a target within a populationof molecules, and more specifically, but not exclusively, to rapiddetection of a non-amplified target.

INTRODUCTION

Detection of a target present at a low concentration and/or at a lownumber in a population of molecules is a well known challenge in manybiological applications.

Bioanalytical systems generally consist of a biosensor and a detectionsystem. The biosensor couples a biological recognition element (e.g., alabeled probe, or a peptide) with specificity to a selected target and aphysical transducer (e.g., a fluorescent source, a metal nano-particleor a radioisotope) that can produce a signal when the biologicalrecognition element binds to the selected target. The detection systemis designed in consideration of the physical transducer employed (e.g.,an optical system detects the fluorescent signal and a scintillationcounter is used to detect a radioisotope).

Previously available approaches which do not amplify the target,include, but are not limited to blotting (e.g. Southern, northern andwestern blotting), immuno-precipitation, in-situ hybridization (e.g.fluorescent in situ hybridization; FISH) and fluorescent activated cellsorting (FACS).

One previously known approach to detection of specific DNA sequencesuses fluorescent dyes as the physical transducer and direct detection ofthe light emitted from the biological sample. Since direct detection ofthe fluorescent light is relatively insensitive, a pre-amplificationphase is often employed (e.g., Rolling circle amplification, Serialinvasive signal amplification reaction). The optical detection is doneby gel electrophoresis or spectrofluorometer. Amplification timesassociated with these techniques typically exceed 1 hour.

A second previously known approach to detection of specific DNAsequences also uses fluorescent dyes as the physical transducer.However, the optical detection is done in the time domain. Populartechniques in this category is Fluorescence Correlation Spectroscopy[Wabuyele et al. (2003) Journal of the American Chemical Society, 125,6937-6945], Two-color fluorescence cross-correlation spectroscopy andusage of confocal fluorescent microscope and measurements of photonburst size, burst duration and fluorescent lifetime. These techniquesusually offer higher sensitivity and faster results than the firstapproach.

Wabuyele et al. [Ibid], for example, employ single pair fluorescenceresonance energy transfer to detect point mutations in unamplifiedgenomic DNA. Normal DNAs are discriminated from mutant (minority) DNAsin heterogeneous populations using allele-specific primers carryingcomplementary stem structures with end-labels. The primers flank thepoint mutation in the target gene and are ligated using a thermostableligase enzyme only when the genomic DNA carries the mutation.

Castro et al. [(1997) Analytical Chemistry, 69, 3915-3920] use twonucleic-acid probes complementary to different sites on a target DNAsequence for detecting specific nucleic acid sequences therein. The twoprobes are labeled with different fluorescent dyes. When mixed with asample containing the target DNA, the probes hybridize to theirrespective binding sites on the same target DNA molecule and theirsignals therefore appear simultaneously. Coincident optical detection ofboth dyes at sufficient sensitivity provides the necessary specificityto detect an unamplified target DNA molecule in a homogeneous assay.

A third previously known approach to detection of specific DNA sequencesuses nano-particles to translate the biorecognition event into ananalytically useful signal. The detection system is either electrical(e.g., measuring the electrical resistance, a MEMS based amperometricdetector as described in, for example Gau et al. ((2001) Biosensors andBioelectronics, 16, 745-755) or optical (e.g., based on colorimetricscatter of gold nanoparticle probes as described in, for exampleStorhoff et al. (2004) Nature Biotechnology, 22, 883-887). These methodsalso offer DNA detection at low concentrations (33 fM). However, thetime associated with these techniques is between 40 min to severalhours.

The following table summarizes the major techniques in the 3 differentapproaches.

DNA Con- centration Reaction The Method [fM] time Remark Open CircleProbes + 500000 ~1 Hour Point Rolling Circle Ampli- mutation fication toenable direct fluorescence detection Serial Invasive Signal Am- 1000copies ~4 Hours Point plification Reaction and mutation directfluorescence detection Ligase Detection Reac- 2.5 ~10 minutes Pointtion + Single Pair FRET mutation using Fluorescence CorrelationSpectroscopy Two-color fluorescence cross 15 >2.5 Hours Pointcorrelation spectroscopy mutation Two-color Single-Molecule 50 >16 HoursSpecific photon burst detection of two Sequence differently labeledprobes detection Single-Molecule photon burst 1000 >20 Hours Specificdetection using confocal Sequence fluorescent microscope detectionSilver-Enhanced gold 500 >6 Hours Point nanoparticle probes and mutationconductivity measurements MEMS based Amperometric 1000 copies 40 minutesSpecific detection using DNA Sequence hybridization and enzyme detectionamplification Gold nanoparticle probes 33 ~2 Hours Specific anddetection using Sequence spectrophotometer detection Gold nanoparticleprobes 50 ~1 Hour Point and detection using mutation spectrophotometer

Some previously available approaches attempt to offset limitations of aspecific probe (e.g. specific activity or fluorescence intensity) byamplifying the target geometrically. Detection of a specific nucleicacid sequence often relies upon amplification of a DNA sequence via thePolymerase Chain Reaction (PCR) for geometric amplification. In somecases, a reverse transcription step is used to transform RNA to DNAwhich is then subject to PCR (RT-PCR). PCR can be subject to limitationsincluding, but not limited to, nonlinearities in amplicon number withcycle number, long optimization and set up times, long run and analysistimes and a high level of inaccuracy and variation (e.g. due tocross-contamination).

Sensitivity of sensing systems is often limited by background noise.

SUMMARY OF THE INVENTION

In an exemplary embodiment of the invention, there is provided a methodof detecting a target within a population of molecules. The methodincludes:

contacting a plurality of labeled probe molecules with the population ofmolecules potentially containing a target of the probe molecules;

acquiring a probe specific signal emitted by the labeled probe moleculesthat bound to the target together with a background signal;

preferentially modulating the probe specific signal by at least one ofmodulating the acquisition and modulating an emission of the probespecific signal; and

detecting the probe specific signal over the background signal using thepreferential modulation.

Optionally, the preferentially modulating includes moving the probemolecules bound to the target in and out of an excitation beam.

Optionally, the preferentially modulating includes temporal modulation.

Optionally, the preferentially modulating includes spatial modulation.

Optionally, the preferentially modulating includes modulation of a pH ofa solution containing the labeled probe molecules.

Optionally, the preferentially modulating includes a single modulationcycle.

Optionally, the preferentially modulating includes multiple modulationcycles.

Optionally, the preferentially modulating includes modifying a responseof the probe molecules bound to the target to an applied excitationenergy.

Optionally, the probe molecules include a molecule type selected fromthe group consisting of a polynucleotide, a polypeptide, a carbohydrateand an ion chelator.

Optionally, the polypeptide includes an antibody.

Optionally, the polynucleotide is selected from the group consisting ofDNA, RNA and synthetic oligonucleotide.

Optionally, the target within the population of molecules includes amolecule type selected from the group consisting of a nucleic acidsequence, an amino acid sequence, a carbohydrate sequence and a featureof a protein determined by non-primary structure.

Optionally, the preferentially modulating includes establishing periodicmotion of the probe molecules bound to the target.

Optionally, the establishing periodic motion includes applying analternating field selected from the group consisting of a magnetic fieldand an electric field to the probe.

Optionally, the probe molecules are attached to a magnetic particle.

Optionally, the probe specific signal is a fluorescent signal.

Optionally, the probe molecules include at least onefluorescence-modifying moiety.

Optionally, the probe specific signal employs an energy transfermechanism selected from the group consisting of fluorescent energytransfer (FET) and fluorescence resonance energy transfer (FRET).

Optionally, the detecting the probe specific signal over the backgroundsignal is accomplished within one minute of the contacting a labeledprobe with the population of molecules.

Optionally, the detecting the probe specific signal over the backgroundsignal is reliably accomplished when no more than 100 copies of thetarget are present.

Optionally, the detecting the probe specific signal over the backgroundsignal is reliably accomplished when a concentration of the target doesnot exceed 1 femtomolar (fM).

Optionally, the detecting includes at least one detection type selectedfrom the group consisting of binary detection, amplitude detection andsynchronous detection.

Optionally, the background signal includes Raman scattering.

Optionally, the preferential modulation produces a probe specific signalwhich is ten times greater in amplitude than the background signal ifthe target is present.

Optionally, the preferential modulation includes increasing a localconcentration of the labeled probe molecules that are bound to thetarget during the acquisition.

In an exemplary embodiment of the invention, there is provided a systemfor detecting a target within a population of molecules. The systemincludes:

a vessel adapted to contain a plurality of labeled probe molecules incontact with a population of molecules potentially containing a targetof the probe molecules;

a fluorescent excitation source adapted to direct an excitation beamthrough the vessel, the beam configured to cause at least some of theprobe molecules that bound to the target to emit a probe specificsignal;

a detector adapted to detect the probe specific signal and produce adetection output;

a signal modulator configured to preferentially modulate at least one ofthe probe specific signal and the detector; and

an analysis module adapted to analyze the detection output inconsideration of the preferential modulation.

Optionally, the analysis module is configured to determine the presenceor absence of the target within the population of molecules.

Optionally, the system includes a modulation indication source adaptedto provide a modulation indication to the signal modulator and to thedetector.

Optionally, the signal modulator is adapted to:

monitor an output of the signal modulator; and

provide a modulation indication to the detector responsive to the outputof the signal modulator.

Optionally, the signal modulator includes an alternating field generatorselected from the group consisting of an electric field generator and amagnetic field generator, the alternating field generator configured toapply power at a level suitable for frequency modulation and sufficientfor moving probe molecules out of the excitation beam.

According to one aspect of the present invention there is provided amethod of detecting or determining nucleic acid sequence of abio-molecule, comprising: hybridizing a labeled probe to thebio-molecule so as to produce a hybridization indicative detectablesignal; establishing a periodic motion to the labeled probe;

detecting the detectable signal synchronously with the periodic motionthereby detecting or determining the nucleic acid sequence of thebio-molecule.

According to further features in preferred embodiments of the inventiondescribed below, the establishing the periodic motion comprises applyingan alternating electric field to the labeled probe.

According to still further features in the described preferredembodiments the labeled probe is attached to a magnetic particle.

According to still further features in the described preferredembodiments the establishing the periodic motion comprises applying analternating magnetic field gradient to the labeled probe.

According to another aspect of the present invention there is provided asystem for detecting or determining nucleic acid sequence of abio-molecule being hybridized to a labeled probe capable of producing ahybridization indicative detectable signal, the system comprising: amechanism for establishing a periodic motion to the labeled probe, themechanism being associated with a transmission unit for transmissiondata characterizing the periodic motion; a detector for detecting thedetectable signal and producing detection signals; and a synchronizer,for synchronizing the detection signals with the periodic motion data,so as to increase signal-to-noise ratio of the detection signals,thereby to detect or determine the nucleic acid sequence of thebio-molecule.

According to further features in preferred embodiments of the inventiondescribed below, the mechanism comprises an alternating electric fieldgenerator.

According to still further features in the described preferredembodiments the mechanism comprises an alternating magnetic fieldgenerator.

According to still further features in the described preferredembodiments the detector comprises a photomultiplier tube.

According to still further features in the described preferredembodiments the detector comprises a radioactive radiation detector.

According to still further features in the described preferredembodiments the system further comprising an excitation unit, configuredfor exciting the hybridization indicative detectable signal.

According to still further features in the described preferredembodiments the labeled probe comprises a fluorescent label having atleast a fluorescence moiety and a fluorescence-modifying moiety, wherebyhybridization of the labeled probe to the bio-molecule detectably altersfluorescence emitted by the fluorescent label.

According to still further features in the described preferredembodiments the fluorescence-modifying moiety comprises a quenchermolecule.

According to still further features in the described preferredembodiments the labeled probe comprises a radioactive label.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Although methods and materialssimilar or equivalent to those described herein can be used in thepractice or testing of the present invention, suitable methods andmaterials are described below. In case of conflict, the patentspecification, including definitions, will control. In addition, thematerials, methods, and examples are illustrative only and not intendedto be limiting.

Implementation of the method and system of the present inventioninvolves performing or completing selected tasks or steps manually,automatically, or a combination thereof. Moreover, according to actualinstrumentation and equipment of preferred embodiments of the method andsystem of the present invention, several selected steps could beimplemented by hardware or by software on any operating system of anyfirmware or a combination thereof. For example, as hardware, selectedsteps of the invention could be implemented as a chip or a circuit. Assoftware, selected steps of the invention could be implemented as aplurality of software instructions being executed by a computer usingany suitable operating system. In any case, selected steps of the methodand system of the invention could be described as being performed by adata processor, such as a computing platform for executing a pluralityof instructions.

For purposes of this specification and the accompanying claims, theterms “label” and “labeled” and their derivatives refer to chemicalmoieties which are provided to contribute to generation of a signal formeasurement. The terms include all signal generating moieties known inthe art. It is expected that during the life of this patent, new signalgenerating moieties will be discovered or characterized and which can beaffected by external modulation and these new signal generating moietiesare incorporated a priori in the terms label and/or labeled.

For purposes of this specification and the accompanying claims, thephrase “probe molecules” indicates any identifiable substance that isused to detect, isolate, or identify another substance (i.e. a target).Probe molecules can be characterized in terms of target specificity.Target specificity is typically in the range of 10⁻³M to 10⁻¹⁵M. “Probemolecules” include, but are not limited to, an aptamer, a labeled strandof DNA that hybridizes with its complementary RNA or a monoclonalantibody that combines with a specific protein.

For purposes of this specification and the accompanying claims, thephrase “probe specific signal” refers to a signal originating from oneor more labels attached to one or more probe molecules that bound totheir target(s).

For purposes of this specification and the accompanying claims, thephrase “background signal” encompasses any signal that is not a probespecific signal.

For purposes of this specification and the accompanying claims,“modulating” and “modulation” indicate varying including but not limitedto varying the frequency and/or amplitude and/or phase.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

Some embodiments of the invention are herein described, by way ofexample only, with reference to the accompanying drawings. With specificreference now to the drawings in detail, it is stressed that theparticulars shown are by way of example and for purposes of illustrativediscussion of embodiments of the invention. In this regard, thedescription taken with the drawings makes apparent to those skilled inthe art how embodiments of the invention may be practiced.

In the drawings:

FIG. 1 is a schematic representation of an exemplary laser excitationsystem for use in the context of some exemplary embodiments of theinvention;

FIG. 2 is a schematic representation of an additional exemplary laserexcitation system for use in the context of some exemplary embodimentsof the invention;

FIG. 3 is a schematic representation of a magnetic modulation system foruse in the context of some exemplary embodiments of the invention;

FIGS. 4a and 4b are histograms of fluorescence as a function ofwavelength for a 6 FAM fluorophore detected directly according toexemplary embodiments of the invention;

FIG. 5 is a histogram illustrating 100% modulation of a photo currentsignal over time according to exemplary embodiments of the invention;

FIG. 6 is a perspective view of an exemplary parabolic tip suitable foruse in exemplary embodiments of the invention;

FIGS. 7a and 7b are video still images of fluorescent output signalconcentrated using an exemplary embodiment of the invention;

FIG. 8 is a simplified flow diagram of a method according to anexemplary embodiment of the invention; and

FIG. 9 is a schematic representation of an exemplary amplification anddetection system according to an embodiment of the invention.

DESCRIPTION OF SPECIFIC EMBODIMENTS OF THE INVENTION

Exemplary embodiments of the invention comprise a method and system fordetecting presence or absence of a target within a population ofbiomolecules. Optionally, the target is indicative of a specificsequence, such as a nucleotide sequence or an amino acid peptidesequence. Exemplary embodiments of the invention employ a probe labeledso as to produce a binding (e.g. hybridization) indicative detectablesignal. The labeled probe can be contacted with a population ofmolecules to analyzer presence and/or amount of a target. Optionally,the label comprises a fluorescent dye and a dark quencher so that whenthe probe contacts the target sequence, the fluorescent dye molecule isdisconnected from the dark quencher and fluorescent light is produced.

Some exemplary embodiments of the invention relate to a method ofdetermining presence or absence of a target within a population ofmolecules. In general, methods according to exemplary embodiments of theinvention employ preferential modulation of probe that has bound to oneor more targets to improve a signal to noise ratio.

According to some embodiments of the invention, improvement in signal tonoise ratio synchronization of signal detection and modulation brings alarger number of labeled probe molecules into an excitation beam at onetime. The larger number of labeled probe molecules contribute to anincrease in probe specific signal. Background signal remains unaffected.

FIG. 8 is a simplified flow diagram of an exemplary method 800.According to exemplary method 800, a plurality of labeled probemolecules are contacted 810 with a population of molecules potentiallycontaining a target of the probe molecules.

Optionally, conditions for contacting 810 are adjusted to favor specifictarget/probe binding and/or to discourage nonspecific binding of theprobe to non-target substrates as is known in the art.

Adjustment of conditions for contacting 810 optionally includesadjustment of temperature and/or adjustment of osmolarity and/oradjustment of detergent concentration and/or adjustment of probe amountand/or adjustment of target amount. In an exemplary embodiment of theinvention, specificity of interaction between target and labeled probecan be confirmed by attempting to dampen a signal using unlabeled probeat a high concentration to saturate available target molecules. Whileexemplary embodiments described herein relate to target and probe insolution, principles described herein are also applicable to techniqueswhere the target is immobilized on a solid substrate (e.g. anitrocellulose or nylon membrane or beads (e.g. agarose or sepharose ora gel)).

According to depicted exemplary method 800, a probe specific signal isthen acquired 820 from labeled probe molecules that bound to the targettogether with a background signal. In exemplary embodiments of theinvention employing laser florescence the background signal comprisesRaman scattering.

In an exemplary embodiment of the invention, once a specific probemolecule has bound to a target molecule, it becomes capable of emittingthe probe specific signal. In some cases, emission of the probe specificsignal continues even if the binding does not continue. In someexemplary embodiments of the invention, preferentially modulatingincludes modifying a response of probe molecules bound to the target toan applied excitation energy.

According to depicted exemplary method 800 preferential modulation 830of the probe specific signal is effected. Preferential modulation maymean that a background signal is modulated less or is not modulated.Optionally, the preferential modulation includes modulating acquisition820 and/or modulating an emission of the probe specific signal.

In an exemplary embodiment of the invention, detecting 840 of the probespecific signal over the background signal uses the preferentialmodulation. Optionally, the preferential modulation contributes to anincrease in sensitivity and/or specificity.

Optionally, the preferential modulation comprises moving the probemolecules bound to the target in and out of an excitation beam.According to various exemplary embodiments of the invention thepreferential modulation comprises temporal modulation and/or spatialmodulation. Optionally, the preferential modulation comprises a singlemodulation cycle or multiple modulation cycles. Optionally, 10, 25, 50,100, 200, 200, 800 or 1200 or intermediate or greater numbers ofmodulation cycles are employed. Optionally, increasing a number ofmodulation cycles contributes to an increase in sensitivity orreliability of detection. Optionally, increasing a number of modulationcycles at a given modulation frequency contributes to an increase indetection time. In some exemplary embodiments of the invention, a signalchange after modulation ceases is informative.

According to various exemplary embodiments of the invention, the probemolecules include molecule types such as nucleic acid (e.g. DNA or RNA),and/or a peptide and/or a protein (e.g. an antibody or a lectin) and/oran ion chelator. Optionally, labeled probes can be provided as DNA orRNA and may be provided as oligomers and/or as restriction fragmentsand/or as amplified PCR products. Restriction fragments can be preparedfrom, for example, genomic DNA, cDNA, plasmids, cosmids, phagemids orphages.

According to various exemplary embodiments of the invention, the targetwithin the population of molecules comprises one or more molecule typesselected from the group consisting of a nucleic acid sequence, an aminoacid sequence, a carbohydrate or carbohydrate sequence, an ion and afeature of a protein determined by non-primary structure (e.g. apost-translational modification, such as tyrosine phosphorylation).

Optionally, method 800 employs a DNA target and a DNA probe, an RNAprobe and a DNA target, a DNA target and a protein probe (e.g. a helixturn helix, a zinc finger, a leucine zipper, a winged helix, an ETSdomain, a helix loop helix, an immunoglobulin fold, a homeodomain and aB3 DNA binding domain), a protein probe and a carbohydrate target (e.g.lectin/carbohydrate pair), a chelator probe and an ion target (e.g.EDTA/Calcium) and or a protein probe and a protein target (e.g.antibody/epitope pair).

U.S. Pat. No. 7,090,995 describes signal generating moieties whichgenerate a signal proportional to an amount of bound ion.

In an exemplary embodiment of the invention, preferentially modulating830 includes establishing periodic motion 850 of the probe moleculesbound to the target. Optionally, establishing periodic motion 850includes applying an alternating field 860 such as a magnetic field 862and/or and an electric field 864 to cause a signal which varies inintensity according to a frequency of the applied field.

In some exemplary embodiments of the invention, probe molecules are eachattached 870 to a magnetic particle. Optionally, attachment 870 of probemolecules to magnetic particles makes the probe molecules more sensitiveto application 860 of an alternating field. In an exemplary embodimentof the invention, probe molecules carrying a magnetic bead which havenot bound to target move in the alternating field according to changesin field polarity but do not contribute to the probe specific signal.

In other exemplary embodiments targets and/or probes and/or moleculesare sufficiently sensitive to the alternating field (e.g. due to aninherent molecular charge) that they can be moved by the alternatingfield without a bead.

According to many exemplary embodiments of the invention, the probespecific signal is a fluorescent signal. Optionally, the probe moleculesinclude at least one fluorescence-modifying moiety. In exemplaryembodiments of the invention, the probe specific signal employs anenergy transfer mechanism. Exemplary energy transfer mechanisms include,but are not limited to, fluorescent energy transfer (FET) andfluorescence resonance energy transfer (FRET).

In an exemplary embodiment of the invention, detecting 840 the probespecific signal over said background signal is accomplished within oneminute 842 of the contacting of labeled probe with the population ofmolecules.

In an exemplary embodiment of the invention, detecting 840 the probespecific signal over said background signal is reliably accomplishedwhen no more than 100 copies of the target are present 844.

In an exemplary embodiment of the invention, detecting 840 the probespecific signal over said background signal is reliably accomplishedwhen a concentration of the target does not exceed 1 femtomolar (fM)846.

In an exemplary embodiment of the invention, use of preferentialmodulation 830 contributes to increased detection sensitivity and/ordetection speed.

According to various exemplary embodiments of the invention, detecting840 includes binary detection and/or amplitude detection and/orsynchronous detection. Binary detection provides a qualitative output(target is or is not present). Amplitude detection provides aquantitative or semi-quantitative indication of target amount.Synchronous detection is a method of detection employs a known pattern(e.g. periodic) of the signal to help decide if there is and/or what thesignal is.

In an experiment exemplifying application of the invention, preferentialmodulation 830 produced a probe specific signal 26 times greater thanthe background at concentration of 3·10⁻¹²M. thereby indicating adetection sensitivity of 1.1·10⁻¹³M. In other exemplary embodiments ofthe invention a factor of 1.001 is employed. In the experiment, 7.2nanomole of a 17 bp DNA probe was labeled with 6-Carboxyfluorescein(6-Fam) and biotin on the same nucleotide at the 5′ end (5′(C6-FAM)/biotin-dTCT). The probe was sequentially diluted in ddH₂O.Streptavidin-coupled magnetic beads with 2.8 μm diameter were used tobind the oligonucleotides. Each bead binds to ˜1938 oligonucleotides. Inorder to demonstrate capability of the detection system, two solutionswere generated.

A “reference solution” contained 75 μl of magnetic beads in bufferTris-HCl at 1.54·10⁻¹⁵M without any fluorescent dye.

A second solution was prepared by first mixing 50 μl of 5.56·10⁻¹⁴Mmagnetic beads with 5·10⁻⁹M of fluorescent labeled DNA probe. After 30min beads connected to the fluorescent labeled DNA were washed andresuspended in 100 μl of a 50:50 mixture of ddH₂O and Tris-HCl buffer.The solution was further diluted to its 1:18 part to produce the “testsolution” containing 1.54·10⁻¹⁵M of magnetic beads and 3·10⁻¹²M offluorescent labeled probes. The reference and test solutions were testedin the detection system.

For this exemplary experiment, laser output power was ˜3.2 mW and thecurrent modulation was performed at ˜6 Hz. It appears that reflectionsof the laser beam from the aggregated beads moving in and out the laserspot were also detected and demodulated by the lock-in amplifier.However, while the produced signal of the “reference solution” (withoutfluorescent molecules) was ˜2 mV, the produced signal of the “testsolution” (with the fluorescent molecules) was ˜52 mV, which yields asignal to noise ratio of ˜26. These preliminary results represent asensitivity of ˜1.1·10⁻¹³M of fluorescent labeled DNA probes. It shouldbe noted that the signal was produced almost immediately (i.e. visuallydiscernible within several seconds).

This exemplary experiment demonstrates both increased sensitivity andincreased rapidity with respect to previously available alternatives.

In an exemplary embodiment of the invention, preferential modulation 830increases a local concentration of labeled probe molecules that arebound to the target during acquisition 820. Optionally, increasing thelocal concentration of labeled probe molecules locally amplifies theprobe specific signal per unit area and/or improves a signal to noiseratio. In an exemplary embodiment of the invention, detecting 840 isperformed where local concentration of is increased.

FIG. 9 is a schematic representation of an exemplary detection system900. In an exemplary embodiment of the invention, system 900 is used todetermine presence or absence of a target, optionally a sequence, withina population of molecules. The molecules and the target are as describedelsewhere in this application.

Depicted exemplary system 900 includes a vessel 910 adapted to contain aplurality of labeled probe molecules in contact with a population ofmolecules potentially containing a target of the probe molecules.Optionally, the contact between the probe molecules and the populationof molecules is established in vessel 910 or prior to introduction invessel 910.

Depicted exemplary system 900 also includes a fluorescence excitationsource 920 adapted to direct an excitation beam 922 through vessel 910.In an exemplary embodiment of the invention, beam 922 is configured tocause at least some of the probe molecules bound to the target to emit aprobe specific signal 924 for acquisition 820.

Depicted system 900 also includes a detector 930 adapted to detect probespecific signal 924 and produce a detection output 932. In an exemplaryembodiment of the invention, detector 930 comprises a PMT.

Optionally, a signal modulator 940 is configured to preferentiallymodulate probe specific signal 924 and detector 930.

In an exemplary embodiment of the invention, an analysis module 970analyzes detection output 932 in consideration of preferentialmodulation. As described hereinabove analysis module 970 can employ, forexample, Binary detection, Amplitude or Synchronous detection.Optionally, analysis module 970 determines presence or absence of thetarget within the population of molecules.

In some exemplary embodiments of the invention, system 900 includes amodulation indication source 960 which provides a modulation indication962 to signal modulator 940 and to detector 930. In an exemplaryembodiment of the invention, modulation indication 962 synchronizesoperation of signal modulator 940 and detector 930.

In other exemplary embodiments of the invention, signal modulator 940monitors its own output 942 and provides a modulation indication 944 todetector 930 responsive to output 942.

Optionally, output 942 and/or or modulation indication 962 comprisemodulation frequency information and/or modulation phase information.

According to some exemplary embodiments of the invention, signalmodulator 940 comprises an alternating field generator (e.g. electricfield generator or magnetic field generator). In an exemplary embodimentof the invention, the alternating field generator applies power at alevel suitable for frequency modulation and/or sufficient for movingprobe molecules out of the excitation beam.

Optionally, analysis module 970 considers whether detection output 932meets or exceeds a predetermined threshold. In some exemplaryembodiments of the invention, the threshold is defined in terms of anamplitude fluctuation during periodic motion produced by signalmodulator 940 and/or in terms of rate of increase of detection output932 as additional bound probe molecules are recruited.

Optionally, analysis module 970 and/or a user of system 900 can changemodulation parameters if detection output 932 does not meet thepredetermined threshold. The user and/or analysis module 970 optionallyinitiate a scan of modulation frequency in order to increase detectionoutput 932. A frequency contributing to an increase in output 932optionally varies with one or more of applied power, distance to traveland probe mechanical behavior.

Exemplary embodiments of the invention are suitable for determiningpresence or absence, and optionally amount, of specific sequence(s)(e.g. nucleic acid and/or peptide and/or carbohydrate) within apopulation of molecules. Described methods and systems of the exemplaryembodiments of the invention efficiently amplify fluorescence from alabeled probe from background fluorescence. This amplificationcontributes to an ability to reliably detect a weak fluorescent signalwithout target amplification. According to exemplary embodiments of theinvention, amplification and detection are performed without separatingthe target from non-target portions of the molecules.

Exemplary systems and methods described herein allow implementation of awide range of biological applications which require detection and/oridentification of specific target sequences, especially at lowconcentrations (e.g. 10⁻¹², 10⁻¹³, 10⁻¹⁴ or 10⁻¹⁵ Molar or lower orintermediate concentrations). For example, systems and methods asdescribed herein can be used for non-invasive method of fetal genotyping(e.g., determination of Rhesus D status, fetal sex, cystic fibrosis andsickle cell anemia) by analysis of fetal DNA presented in the plasma ofpregnant women and/or for determining chick gender in ovo and/or foranalysis of molecular markers associated with various diseases (e.g.different types of cancer, HIV, rabies, hoof and mouth disease and prionmediated diseases) in non-fetal tissue and/or for pathogen (e.g., E.coli., C. botulinum and B. anthracis) detection in environmental samplesor food samples.

In an exemplary embodiment of the invention, non-invasive fetalgenotyping as described hereinabove can replace or augment assays whichrely upon sampling of embryonic fluid.

According to various exemplary embodiments of the invention, target sizevaries. Optionally, a target can be as small as a single nucleotidemutation or as large as a chromosomal region. Optionally, a probespecific to a small target is used as indicative of changes in achromosomal region.

In an exemplary embodiment of the invention, early detection of diseaseassociated markers using exemplary embodiments of the invention cancontribute to increased therapy efficacy and/or increased averagesurvival time.

According to previously available alternatives, chick gender isdetermined post hatching, most often manually by a feathering technique.Exemplary embodiments of the invention can be employed to determinechick gender in ovo. Early gender determination in ovo can reduce costsin the poultry industry, for example by allowing elimination of anon-desired gender from an incubation cycle at an early stage. It isenvisioned that operational costs of incubation could be reduced by asmuch as 30 to 50% in this way. This approach has utility in the eggindustry, as well as in breeding programs where separate male and femalelines are produced for subsequent cross breeding.

From the humanitarian standpoint, in ovo gender determination of poultrycan prevent massive killing of new born male chicks in the layerindustry. The system and method of the present embodiments can also beused in many other applications, including, without limitation, rapiddetection of pathogenic (e.g., Bacillus anthracis) in environmentalsamples, and the like.

According to many exemplary embodiments of the invention, signalmodulator 940 causes modulation of probe specific signal 924 and/ordetector 930 with a frequency of 1-10 Hz.

Optionally, a higher frequency can be employed (e.g. 100. 1000 or 10,000Hz or intermediate or higher frequencies). Optionally, a higherfrequency can compensate for instability of excitation beam 922. In anexemplary embodiment of the invention, multiple modulations within astable time contribute to the compensation. In an exemplary embodimentof the invention, a frequency is selected so that a combination offrequency and power has no significant biological and/or chemicaleffect.

Optionally, a lower freq, (e.g. 0.1 Hz) is employed. In an exemplaryembodiment of the invention, a lower frequency can be employed despiteinstability of excitation beam 922. Optionally, monitoring ofinstability of excitation beam 922 can be used as an input foradditional signal processing, for example, for amplitude correction

In an exemplary embodiment of the invention, method 800 and/or system900 do not move water. Optionally, method 800 and/or system 900 can bemodified to move water, if advantageous. It may be advantageous to movewater if for example, spinning, concentrates the probe.

In an exemplary embodiment of the invention, modulation can cause changeof light polarization. Optionally, polarization can be detected using ananalyzing polarizer. In an exemplary embodiment of the invention, aprobe with polarizable modulation is employed.

In some exemplary embodiments of the invention modulation is achieved byspatial arrangement. For example, a standing acoustic wave orcentrifugation can arrange beads or targets in a pattern. This patterncan be detected by moving the laser beam or by its expected Braggdiffraction/scattering, which is at a specific angle. Alternatively, oradditionally, the acoustic wave can be used to move the beads.

While exemplary embodiments of the invention are explained herein indetail, it is to be understood that the invention is not limited in itsapplication to the details of construction and the arrangement of thecomponents set forth in this specification description or illustrated inthe drawings. The invention is capable of other embodiments or of beingpracticed or carried out in various ways. Also, it is to be understoodthat the phraseology and terminology employed herein is for the purposeof description and should not be regarded as limiting.

As used herein, “nucleic acid” refers to DNA, RNA, single-stranded ordouble-stranded and any chemical modifications thereof. Modificationsinclude, but are not limited to, those which provide other chemicalgroups that incorporate additional charge, polarizability, hydrogenbonding, electrostatic interaction, and functionality to the nucleicacid. Such modifications include, but are not limited to, 2′-positionsugar modifications, 5-position pyrimidine modifications, 8-positionpurine modifications, modifications at exocyclic amines, substitution of4-thiouridine, substitution of 5-bromo or 5-iodo-uracil; backbonemodifications, methylations, unusual base-pairing combinations such asthe isobases isocytidine and isoguanidine and the like. Modificationscan also include 3′ and 5′ modifications such as capping.

As used herein, “fluorescent molecule” or “fluorescent moiety” refers toa molecule or molecules that, when excited with light having a selectedwavelength, emits light of a different wavelength. Fluorescent moleculesor moieties may also be referred to as “fluorophores”.

As used herein, “fluorescence-modifying molecule” or“fluorescence-modifying moiety” refers to a molecule or molecules thatcan alter in any way the fluorescence emission from a fluorescentmolecule or moiety. A fluorescence-modifying molecule or moietygenerally accomplishes this through an energy transfer mechanism.Depending on the identity of the fluorescence-modifying molecule ormoiety, the fluorescence emission can undergo a number of alterations,including, but not limited to, attenuation, complete quenching,enhancement, a shift in wavelength, a shift in polarity, a change influorescent lifetime. One example of a fluorescence-modifying moleculeor moiety is a quenching molecule or moiety.

As used herein, “quenching molecule” or “quenching moiety” refers to anyfluorescence-modifying molecule or moiety that can attenuate at leastpartly the light emitted by a fluorescent molecule or moiety. Thisattenuation is referred to herein as “quenching”. Hence, illumination ofthe fluorescent molecule or moiety in the presence of the quenchingmolecule or moiety leads to an emission signal that is less intense thanexpected, or even completely absent. Quenching occurs through energytransfer between the fluorescent molecule or moiety and the quenchingmolecule or moiety

As used herein, “energy transfer” refers to the process by which thefluorescence emission of a fluorescent molecule or moiety is altered bya fluorescence-modifying molecule or moiety. Fluorescence emission fromthe fluorescent molecule or moiety is attenuated (quenched) if thefluorescence-modifying molecule or moiety is a quenching molecule ormoiety. Energy transfer can occur through fluorescence resonance energytransfer, or through direct energy transfer. The exact energy transfermechanisms in these two cases are different. It is to be understood thatany reference to energy transfer in the instant application encompassesall of these mechanistically-distinct phenomena. Energy transfer is alsoreferred to herein as fluorescent energy transfer or FET.

As used herein, “energy transfer pair” refers to any two molecules thatparticipate in energy transfer. Typically, one of the molecules acts asa fluorescent molecule, and the other acts as a fluorescence-modifyingmolecule. The preferred energy transfer pair of the instant inventioncomprises a fluorescent molecule and a quenching molecule. In somecases, the distinction between the fluorescent molecule and thefluorescence-modifying molecule may be blurred. For example, undercertain circumstances, two adjacent fluorescein molecules can quench oneanother's fluorescence emission via direct energy transfer. For thisreason, there is no limitation on the identity of the individual membersof the energy transfer pair in this application. All that is required isthat the spectroscopic properties of the energy transfer pair as a wholechange in some measurable way if the distance between the individualmembers is altered by some critical amount.

“Energy transfer pair” is used to refer to a molecule of molecules thatform a single complex within which energy transfer occurs. Suchcomplexes may comprise, for example, two fluorescent molecules which maybe different from one another and one quenching molecule, two quenchingmolecules and one fluorescent molecule, or multiple fluorescentmolecules and multiple quenching molecules. In cases where there aremultiple fluorescent molecules and/or multiple quenching molecules, theindividual molecules may be different from one another.

As used herein, “fluorescence resonance energy transfer” or “FRET”refers to an energy transfer phenomenon in which the light emitted bythe excited fluorescent molecule is absorbed at least partially by afluorescence-modifying molecule. If the fluorescence-modifying moleculeis a quenching molecule, then that molecule can either radiate theabsorbed light as light of a different wavelength, or it can dissipateit as heat. FRET depends on an overlap between the emission spectrum ofthe fluorescent molecule and the absorption spectrum of the quenchingmolecule. FRET also depends on the distance between the quenchingmolecule and the fluorescent molecule. Above a certain criticaldistance, the quenching molecule is unable to absorb the light emittedby the fluorescent molecule, or can do so only poorly.

As used herein “direct energy transfer” refers to an energy transfermechanism in which passage of a photon between the fluorescent moleculeand the fluorescence-modifying molecule does not occur. Without beingbound by a single mechanism, it is believed that in direct energytransfer, the fluorescent molecule and the fluorescence-modifyingmolecule interfere with each others electronic structure. If thefluorescence-modifying molecule is a quenching molecule, this willresult in the quenching molecule preventing the fluorescent moleculefrom even emitting light.

In general, quenching by direct energy transfer is more efficient thanquenching by FRET. Indeed, some quenching molecules that do not quenchparticular fluorescent molecules by FRET (because they do not have thenecessary spectral overlap with the fluorescent molecule) can do soefficiently by direct energy transfer. Furthermore, some fluorescentmolecules can act as quenching molecules themselves if they are closeenough to other fluorescent molecules to cause direct energy transfer.For example, under these conditions, two adjacent fluorescein moleculescan quench one another's fluorescence effectively. For these reasons,there is no limitation on the nature of the fluorescent molecules andquenching molecules useful for the practice of this invention.

In achieving specific target (e.g. DNA sequence or epitope) a high levelof noise caused by non-specific fluorescence (e.g. from scattering oflight from the solution) coupled with a low level of fluorescent signalis a common problem. Nonetheless, fluorescent detection withoutamplification of the target offers a way to avoid problems associatedwith PCR and/or to detect non-nucleic acid targets. In an exemplaryembodiment of the invention, fluorescence resonance energy transfer(FRET) is used to provide a signal indicative of target/probe binding ata level well above background.

In various exemplary embodiments of the invention a probe is labeled soas to produce a hybridization indicative detectable signal and contactedwith a population of molecules being analyzed for presence of a target.A representative example of a labeled probe suitable for the presentembodiments, includes, without limitation, TaqMan® probe labeled with afluorescent dye and a dark quencher. The labeled probe can be used todiscriminate the target sequence. When the target sequence is detected,the fluorescent dye molecule is disconnected from the dark quencher andfluorescent light is produced. FIG. 1 illustrates schematically a laserexcitation system 100 for use in the context of some exemplaryembodiments of the invention.

In FIG. 1, an excitation laser beam 130 is focused, optionally by meansof a mirror 140, through by a microscope objective 150 into a cuvette110 containing a sample comprising a population of molecules in solutionand a labeled probe. The cuvette can be, for example a 2×2 mm squarecross section quartz cell.

In an exemplary embodiment of the invention, cuvette 110 comprises twoelectrode poles 112 and 114 connected to a high voltage modulator 116.Optionally, modulator 116 applies an AC voltage with a defined frequencyto poles 112 and 114. In an exemplary embodiment of the invention, thefrequency is less than 60, optionally 40, optionally 20, optionally 10,optionally 5, optionally 3, optionally 2 optionally 1 Hz or intermediatevalues.

In an exemplary embodiment of the invention, a labeled probe comprises anucleic acid probe (e.g. oligonucleotide or restriction fragment or PCRproduct) characterized by a negative charge. Optionally, the negativecharge of the probe causes a fluorescent label attached to the probe tomove orthogonally in and out of a beam from laser 130 according to thefrequency of modulator 116. The orthogonal motion causes pulses of lightwhich emanate from cuvette 110 towards a detection unit 120 (e.g. aphotomultiplier (PMT)) and optionally demodulated by a Lock-In Amplifier160. Synchronous detection dramatically decreases problems associatedwith background noise (e.g., Raman scattering of the solvent) andpotentially increases detection sensitivity by two orders of magnitudeor more.

In the depicted embodiment, light emanating from cuvette 110 passesthrough one or more optional elements including, but not limited to, afocusing lens 126, a spatial or spectral filter (e.g. a slit) 124 and abandpass filter 122.

FIG. 2 illustrates schematically another laser excitation system 200 foruse in the context of other exemplary embodiments of the invention. Insystem 200, microscope objective 150 and optional mirror are replaced bya focusing lens 226.

Optionally, system 100 and/or 200 can be configured to perform automatedand/or a manual analysis of light arriving at detector 120. Manualevaluation can be performed, for example, by visual evaluation of animage on a display screen.

Modulation of the fluorescent dye can also be done by a sinusoidalmagnetic field gradient (e.g., using two coils [Katsura et al. (2001)Superconductor Science and Technology, 14, 1131-1134]). According toexemplary embodiments of the invention employing this technique, thelabeled probe (e.g., TaqMan® probe) is double labeled with a fluorescentdye and Biotin on the same nucleotide at the 5′ end. The dark quencheris connected at the 3′ end. When the target DNA sequence is detected,the fluorescent dye molecule, still connected to the biotin, isseparated from the dark quencher and fluorescent light can be produced.The biotin is attached to streptavidin-coupled magnetic beads. Theexternal magnetic modulation sets the fluorescent molecule, which isconnected via the biotin and avidin to magnetic particles, in asinusoidal motion. The sinusoidal motion, in and out of the orthogonallaser beam, produces a sinusoidal pulse of fluorescent light which iscollected by the PMT and demodulated by a Lock-In Amplifier.

FIG. 3 depicts an exemplary embodiment of a magnetic modulation system300 suitable for use in the context of some embodiments of theinvention. In system 300 a beam emanating from laser 130 passes throughbeam splitter 340 and is directed, optionally via microscope objective150, to cuvette 110 containing the solution with biomolecules comprisingtarget and the labeled probe. Fluorescent light created by laserexcitation of the labeled probe travels back though beam splitter 340,optionally via microscope objective 150) to detector 120 (depicted as aPMT). In the depicted embodiment, electrodes 112 and 114 are replaced byelectromagnetic poles 312 and 314 and voltage modulator 116 is replacedby current modulator 316. Optionally, output from PMT 120 regulatescurrent modulator 316 via lock in amplifier 160.

In some embodiments, magnetic modulation system 300 is more efficientthan system 100 and/or system 200. In an exemplary embodiment of theinvention, the magnetic gradient created by electromagnetic pole (312 or314) attracts all the magnetic particles in the solution and forms avery narrow path between the two poles. For example, in a 50 microlitter solution containing 1×10⁻¹³ Molar target (connected to magneticparticles), all 3,000,000 target molecules (e.g. specific DNA sequences)are collected in a narrow line between the poles. Optionally, thiscollection creates a high intensity fluorescent signal which contributesto an ability to detect a low target concentration in the presence ofbackground fluorescence.

Additional objects, advantages and novel features of the presentinvention will become apparent to one ordinarily skilled in the art uponexamination of the following examples, which are not intended to belimiting. Additionally, each of the various embodiments and aspects ofthe present invention as delineated hereinabove and as claimed in theclaims section below finds experimental support in the followingexamples.

EXAMPLES

Reference is now made to the following examples, which together with theabove descriptions illustrate the invention in a non limiting fashion.

As noted above, direct detection of fluorescent light is limited by thebackground noise contributed mainly by the light scattered from thesolvent (e.g. elastic Rayleigh scattering of the laser wavelength andred shifted Raman scattering). Residual fluorescence increases rapidlywith the energy of the exciting photon. Thus working in the red part ofthe spectrum will reduce the background problem. A rough estimation forthe direct detection limitation due to Raman scattering is considered inthe following calculation. An excitation laser beam (Argon laser model262A-01, λ=488 nm, output power P=1 mW, beam waist ω=20 μm) is focusedinto a 0.5×5 mm (I.D) large ratio rectangle borosilicate tube filledwith water based buffer and 6-FAM (6-Carboxyfluorescein) as thefluorescent dye. In water, the dominant Raman line is produced by thefundamental O—H stretch mode of the water molecule. The Raman frequencyshift is 3400 cm⁻¹ (i.e. for excitation laser wavelength at 488 nm, theRaman peak is at 585 nm) and the cross section is:

$\sigma = {4{\pi \cdot 8.2 \cdot {10^{- 34}\left\lbrack \frac{m^{2}}{molecule} \right\rbrack}}}$The detection volume is:V=π·r ² ·L=π(20 μm)²·5 mm=6.28·10⁻⁹ [litter]The Laser Intensity is:

$I = {\frac{P}{A} = {\frac{1\mspace{11mu}{mW}}{\pi \cdot \left( {20\mspace{14mu}{\mu m}} \right)^{2}} = {795774\left\lbrack \frac{W}{m^{2}} \right\rbrack}}}$The Number of water molecule in the detection volume is:N=C·V·N _(a)=55.5 Molar·6.28·10⁻⁹ litter·6.02·10²³=2.1·10¹⁷ [molecules]The Photon absorption rate of single molecule water at 488 nm is:

${W = {\frac{\sigma \cdot I}{h \cdot \upsilon} = {\frac{\sigma \cdot I \cdot \lambda}{h \cdot c} = {\frac{4{\pi \cdot 8.2 \cdot 10^{- 34} \cdot 795774 \cdot 488 \cdot 10^{- 9}}}{6.62 \cdot 10^{- 34} \cdot 3 \cdot 10^{8}} = {2.01 \cdot {10^{- 8}\left\lbrack \frac{photons}{\sec} \right\rbrack}}}}}}\quad$The Photon emission rate of all water molecules is (assuming the quantumefficiency is 1):

${\overset{\_}{W} = {{{W \cdot {N2}}{{.01} \cdot 10^{- 8} \cdot 2.1 \cdot 10^{17}}} = {4.22 \cdot {10^{9}\left\lbrack \frac{photons}{\sec} \right\rbrack}}}}\quad$

Inhomogeneous broadening of Raman linewidth results with less than0.0001 of peak power at detection bandwidth (515-565 nm). Thus, thetotal Photon emission rate of all water molecules at the range 515-565nm is:

${\overset{\_}{W}}_{Water} = {{\overset{\_}{W} \cdot 0.0001} = {4.22 \cdot {10^{5}\left\lbrack \frac{photons}{\sec} \right\rbrack}}}$

Photon Emission Rate of the Fluorescent Dye (6-FAM)

Assuming extinction coefficient ε=83000[1/(Molar·cm)], the absorptioncross section of 6-FAM is (Beer Lambert Law):

${{\sigma = {\frac{{\ln(2)} \cdot 1000}{{\log(2)} \cdot N_{a}} \cdot {ɛ\left\lbrack \frac{1}{{Molar} \cdot {cm}} \right\rbrack}}}\quad} = {{3.17 \cdot {10^{- 16}\left\lbrack {cm}^{2} \right\rbrack}} = {3.17 \cdot {10^{- 20}\left\lbrack m^{2} \right\rbrack}}}$Hence, the photon absorption rate of a single 6-FAM molecule is:

${W = {\frac{\sigma \cdot I \cdot \lambda}{h \cdot c} = {\frac{3.17 \cdot 10^{- 20} \cdot 795774 \cdot 488 \cdot 10^{- 9}}{6.62 \cdot 10^{- 34} \cdot 3 \cdot 10^{8}} = {61985\left\lbrack \frac{photons}{\sec} \right\rbrack}}}}\quad$

In order to achieve signal to noise ratio of √{square root over(SNR)}=10, the fluorescent emission rate of the 6-FAM should be at least100 times higher than water:

${\overset{\_}{W}}_{6\text{-}{FAM}} = {{{\overset{\_}{W}}_{Water} \cdot 100} = {4.22 \cdot {10^{7}\left\lbrack \frac{photons}{\sec} \right\rbrack}}}$

Therefore, assuming fluorescent quantum yield of ϕ_(F)=0.9, the numberof the 6-FAM molecules should be:

$N = {\frac{\overset{\_}{W}}{\phi_{F} \cdot W} = {\frac{4.22 \cdot 10^{7}}{0.9 \cdot 61985} \cong {756\lbrack{molecules}\rbrack}}}$

A rough estimation of the minimal concentration for direct detection(assuming √{square root over (SNR)}=10) is:

$C = {\frac{N}{V \cdot N_{a}} = {\frac{756}{6.02 \cdot 10^{23} \cdot 6.28 \cdot 10^{- 9}} \cong {2 \cdot {10^{- 13}\lbrack{Molar}\rbrack}}}}$

For example, the limitation of commercially available detection systems:

(1) Molecular Devices, SpectraMax M5: Intensity detection limit 5·10⁻¹²Molar.

(2) Molecular Devices, Analyst HT: Intensity detection limit 5·10⁻¹²Molar.

FIGS. 4a and 4b show results from a direct detection experiment of 6-FAMat different concentrations. FIG. 4b shows the excitation laser at 488nm and several emission spectra of different 6-FAM concentrations. FIG.4b clearly shows the 585 nm peak of pure water emission spectrum. FIG.4a depicts the emission spectra confined by spectral filters to thewavelength range of 515-565 nm. Pure water and 1·10⁻¹³ Molar of 6-FAMresults with the same level of emission when the emission wavelength islimited. FIGS. 4a and 4b demonstrate that limitation of wavelength viaspectral filtering to exclude background fluorescence from water is nothelpful at target concentrations at or below 10⁻¹³ Molar, although itcan be useful at higher concentrations.

As noted above, the modulation motion of the fluorescent dye in and outthe orthogonal laser beam produces a regular signal at the PMT (e.g.sinusoidal or other wave form). In an exemplary embodiment of theinvention, the regular signal contributes to an improvement indemodulation. The effect of modulation centers the signal at themodulation frequency rather than at DC, in some cases reduces 1/f noiseand separates the signal from the background residual fluorescence.

The shot noise limitation of synchronous detection using a Lock-InAmplifier can be calculated assuming 100% modulation of the photocurrent signal.

In some cases, a maximum value is what is shown in FIG. 5 as DC, but itcan depend on implementation. Alternatively, or additionally, a laserexcitation beam laser can be aimed at either where probe molecules areexpected to be, or where the probe molecules are expected not to be.

As shown in FIG. 5:

The average photocurrent is:

$I_{DC} = \frac{I_{\min} + I_{\max}}{2}$The shot noise:I _(noise)=√{square root over (2·e·I _(DC) ·B)}Where B is the detection bandwidth of the Lock-In Amplifier (B≈1 Hz)

In order to achieve signal to noise ratio of √{square root over(SNR)}=10, the signal should be:

${SNR} = {\frac{I_{DC}}{I_{noise}} = {\frac{I_{DC}}{\sqrt{2 \cdot e \cdot I_{DC} \cdot B}} = 10}}$Hence$I_{DC}^{\min} = {\left( {10 \cdot \sqrt{2 \cdot e \cdot B}} \right)^{2} = {{200 \cdot 1.6 \cdot 10^{- 19} \cdot 1} = {3.2 \cdot {10^{- 17}\lbrack A\rbrack}}}}$

The energy of 520 nm photons (peak emission wavelength of 6-FAM) is:

${{h\;\upsilon} = {{h \cdot \frac{c}{\lambda}} = {{6.62 \cdot 10^{- 34} \cdot \frac{3 \cdot 10^{8}}{520 \cdot 10^{- 9}}} = {3.82 \cdot {10^{- 19}\lbrack{joule}\rbrack}}}}}\quad$

Assuming the PMT has quantum yield of η=0.2, the total rate of photonsarriving the PMT is:

$W = {\frac{3.2 \cdot {10^{- 17}\lbrack A\rbrack}}{3.82 \cdot {10^{- 19}\lbrack{joule}\rbrack} \cdot 0.2} \cong {420\left\lbrack \frac{photons}{\sec} \right\rbrack}}$

Using a microscope lens (25.4 mm diameter, 16 mm focal length andNumerical Aperture 0.25) to image the detection area to the PMTeffective area, the collection efficiency is ˜1.5%. Therefore, the totalnumber of photons emitted from the detection area is:

$\overset{\_}{W} = {\frac{W}{0.015} = {28\text{,}{000\left\lbrack \frac{photons}{\sec} \right\rbrack}}}$

Given the same laser source (Argon laser model 262A-01, λ=488 nm, outputpower P=1 mW, beam waist ω=20 μm), The number of molecules required is:

$N = {\frac{\overset{\_}{W}}{\phi_{F} \cdot W} = {\frac{28000}{0.9 \cdot 61985} \cong 0.5}}$

As noted above, a potential advantage of magnetic modulation is thecondensation of all the magnetic beads in a small area where the laserbeam is focused on. Hence, assuming a 50 micro litter tube andcondensation efficiency of 1% (i.e. only 0.01 of the beads are condensedto the laser beam), a rough estimation of the minimal concentration forsynchronous detection (assuming √{square root over (SNR)}=10) is:

$C = {\frac{N}{V \cdot N_{a}} = {\frac{0.5}{6.02 \cdot 10^{23} \cdot 50 \cdot 10^{- 6} \cdot 0.01} \cong {1 \cdot {10^{- 18}\lbrack{Molar}\rbrack}}}}$

The following experiment was taken in order to demonstrate and visualizethe ability of two electromagnetic poles to maneuver small magneticparticles (Dynabeads, M-280, Invitrogen, Carlsbad, Calif.)) in 1-Dmovement, in and out the laser beam. A 488 nm air cooled argon laser(262A-01 power supply, Spectra-Physics Lasers, Mountain View, Calif.)was used as an excitation light source. The laser beam is directed usinga 506 nm long-pass filter (LPF-506-25.222 mm×35.6 mm-HC, CVI Laser,Albukuerque, N. Mex.) into a microscope objective lens (M-10×, 0.25 N.A,16.5 mm Focal length, Newport Corporation, Irvine, Calif.) which focusthe laser beam into a 500 μm wide borosilicate glass tube (RT4905,0.5×5.0 mm Internal Dimensions, 0.3 mm wall width, Vitrocom, MountainLakes, N.J.). The emitted light from the sample is collected using thesame microscope objective lens, transmitted through the long-pass filterand detected by a CCD camera (Pl-A741, 1.3 Mega pixels, Pixelink,Ottawa, Canada).

In order to achieve high forces on relatively small magnetic beads, highmagnetization saturation material can be used to construct the poles(e.g. M5, 0.3 mm thick, grain oriented silicon steel, 1.9 Tesla). In anexemplary embodiment of the invention, parabolic shaped pole tipscontribute to an additional increase in field gradient outside thepoles. An exemplary parabolic tip is depicted in FIG. 6. Optionally, twoidentical 4500 wound coils (wire diameter 0.71 mm) with the polesinside, are placed on an XYZ translation stages (e.g. M-462-XYZ-M,Newport, Irvine, Calif.), one at each side of a rectangular tube.

FIGS. 7a and 7b depict results from an experiment in which a samplecomprising 2.5·10⁻¹⁵ Molar of small magnetic particles (M-280,Dynabeads) at 50 μlitter Tris-HCl buffer is subject to excitation with alaser beam. The photographs illustrate a sequence of events which occursas modulation of current applied to the two coils creates a cyclicmagnetic field gradient. The cyclic magnetic field gradient initiallyattracts magnetic beads to one pole (FIG. 7a , left side). As polarityof the magnetic field gradient is reversed, a cloud of condensedmagnetic beads cross path of the excitation laser beam (FIG. 7b ,center) and eventually pass to the second pole. A periodicity with whichthe light of FIG. 7b appears will vary with a frequency of cycling ofcurrent between the two poles.

For the experiment depicted in FIGS. 7a and 7b current was applied withat 1.35 A with a frequency of 6 Hz. This pair of pictures was made usinga probe which was not bound to beads or to a target. An air-cooled argonlaser with an excitation wavelength of 488 nm was employed and noquenching system was employed.

In order to apply high forces on relatively small magnetic beads, veryhigh magnetization saturation material is optionally used to constructthe poles (M5, 0.3 thick, grain oriented silicon steel, 1.9 Tesla). If alow magnetization saturation material is employed, applied forces willbe lower and time for the magnetic field to move the beads will belonger. In embodiments using a low magnetization saturation material, alower frequency can compensate for the longer time.

Further increase of the field gradient outside the poles is achievedusing parabolic shaped pole tips. Two identical 4500 wound coils (0.71mm wire diameter) with the poles inside, are placed on XYZ translationstages; one at each side of the rectangle tube. In order to maneuver themagnetic beads in a periodic 1-D movement a current modulator whichproduces successively 1.35 A to each coil at frequencies of 1-6 Hz canoptionally be employed. The resulting magnetic field at the poles tipsusing such an optional configuration was measured to be ˜0.7 Tesla.

It is appreciated that certain features of the invention, which are, forclarity, described in the context of separate embodiments, may also beprovided in combination in a single embodiment. Conversely, variousfeatures of the invention, which are, for brevity, described in thecontext of a single embodiment, may also be provided separately or inany suitable subcombination.

Although the invention has been described in conjunction with specificembodiments thereof, it is evident that many alternatives, modificationsand variations will be apparent to those skilled in the art.Accordingly, it is intended to embrace all such alternatives,modifications and variations that fall within the spirit and broad scopeof the appended claims. All publications, patents and patentapplications mentioned in this specification are herein incorporated intheir entirety by reference into the specification, to the same extentas if each individual publication, patent or patent application wasspecifically and individually indicated to be incorporated herein byreference. In addition, citation or identification of any reference inthis application shall not be construed as an admission that suchreference is available as prior art to the present invention.

What is claimed is:
 1. A method of detecting at least one targetmolecule within a population of molecules, the method comprising:contacting a plurality of probe molecules, selected to bind specificallywith the target molecule, each probe molecule labeled with at least onefluorescent molecule, with the population of molecules containing atleast one of said target molecule, where at least one probe moleculebinds to at least one target molecule; contacting the plurality of probemolecules with magnetic beads, wherein the at least one probe moleculethat binds to the target molecule, or a part of that probe molecule,also binds to one of the magnetic beads via an intermediary component;forming a cloud of the magnetic beads, condensed; illuminating the cloudof magnetic beads with an excitation beam that produces fluorescentemission from the fluorescent molecules labeling the probe molecules orparts of probe molecules bound to the magnetic beads; acquiring abackground signal and a signal of the fluorescent emission; detectingthe fluorescent emission signal over the background signal; anddetermining from the detected fluorescent emission signal, one or bothof a presence of the target molecule within the population of molecules,and an amount of the target molecules within the population ofmolecules; wherein the method is an energy transfer-based assay, whereinat least one of the probe molecules includes a probe molecule labeledwith at least one or more fluorescent molecules at a first end thereofand having one or more quenching molecules at a second end thereof; andwherein, prior to detecting the fluorescent signal, the one or morefluorescent molecules are separated from the one or more quenchingmolecules.
 2. The method according to claim 1, wherein said contacting aplurality of probe molecules with the population of moleculespotentially containing at least one of said target molecule includes atleast one probe molecule selectively binding to at least one targetmolecule.
 3. The method according to claim 1, wherein said contactingthe plurality of probe molecules with magnetic beads includes at leastone magnetic bead selectively binding with a probe molecule via at leastone intermediary component.
 4. The method according to claim 1, whereinthe intermediary component is one or more of the following: biotin, aDNA sequence, an RNA sequence, an antibody, a protein, and a targetmolecule.
 5. The method according to claim 1, wherein the at least oneprobe molecule binds with the target molecule before the magnetic beadbinds with the probe molecule or part of the probe molecule via anintermediary component.
 6. The method according to claim 1, wherein theat least one probe molecule binds with the target molecule after themagnetic bead binds with the probe molecule or part of the probemolecule via an intermediary component.
 7. The method of claim 1,wherein the one or more fluorescent molecules are separated from the oneor more quencher molecules by PCR (polymerase chain reaction).
 8. Themethod according to claim 1, wherein the method is a sandwich-basedassay, wherein a capture probe, labeled with a portion of theintermediary component, and a signaling probe, labeled with afluorescent molecule, hybridize to the target molecule.
 9. The method ofclaim 1, wherein the fluorescent signal is detected by a CCD camera. 10.The method according to claim 1, wherein said at least one targetmolecule includes at least one molecule type selected from the groupconsisting of a nucleic acid sequence, an amino acid sequence, acarbohydrate, a carbohydrate sequence, an ion, and a feature of aprotein determined by non-primary structure.
 11. The method according toclaim 1, wherein at least some of said plurality of probe moleculesinclude at least one of nucleic acids, peptides, proteins, antibodies,and ion chelators; and wherein at least some of said plurality of targetmolecules include at least one molecule type selected from the groupconsisting of a nucleic acid sequence, an amino acid sequence, acarbohydrate, a carbohydrate sequence, an ion, and a feature of aprotein determined by non-primary structure.
 12. The method according toclaim 1, wherein said at least one probe molecule bound to said at leastone target molecule includes at least one protein molecule bound to oneprotein target.
 13. The method according to claim 1, wherein said atleast one probe molecule bound to said at least one target moleculeincludes at least one nucleic acid molecule bound to a nucleic acidtarget.
 14. The method according to claim 1, wherein said at least oneprobe molecule bound to said at least one target molecule includes atleast one antibody bound to an epitope.
 15. The method according toclaim 1, wherein the intermediary component through which the probemolecule or part of the probe molecule binds to one of the magneticbeads does not comprise any part of the target molecule.
 16. The methodaccording to claim 1 wherein at least a first portion of said pluralityof probe molecules each have a fluorescent label and are bound to atarget and wherein at least a second portion of said probe molecules areeach attached to a magnetic bead and are bound to the same target. 17.The method according to claim 16, wherein the probe molecules bound tothe target molecules include at least one protein molecule bound to oneprotein target.
 18. The method according to claim 16, wherein the probemolecules bound to the target molecules include at least one nucleicacid molecule bound to a nucleic acid target.